Sun Oct 9 16:16:34 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 16:16:34 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6215410 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -21.95800 35.12600 ymin,ymax (A): 55.13300 107.5630 zmin,zma (A): -2.364000 54.91300 x,y,z range (A): 57.08400 52.43000 57.27700 scale (grids/A): 0.6215410 object centre (A): 6.584000 81.34800 26.27450 number of atom coordinates read : 3070 total number of charged atoms : 2928 net assigned charge : -3.499987 assigned positive charge : 457.8630 centred at (gu) : 90.93411 90.14705 89.98444 assigned negative charge : -461.3643 centred at (gu) : 90.94719 90.02309 90.11096 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7833 nv = 96 ne = 84 npr = 62466 no. pairs analyzed = 62466 no. exposed pairs = 4001 no. arc points = 27695 no. surface atoms = 1346 nbur = 1724 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 4132 m= 4 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2300000 number of dielectric boundary points 4081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2798 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9703 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3841817E-09 -1.3498709E-08 midg,1,midg; midg,igrid,midg -1.2901394E-08 7.3977682E-09 1,midg,midg; igrid,midg,midg -1.5424269E-09 -4.9308038E-09 gauss-seidel spectral radius is 0.9866384 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 16:16:34 rms-change max change #iterations 0.1395632 20.03757 at 10iterations 1.2879180E-02 1.678827 at 20iterations 1.2520824E-03 0.1752443 at 30iterations 1.4470935E-04 1.9789934E-02 at 40iterations 2.9865108E-05 3.1385422E-03 at 50iterations finished qdiffx linear iterations at : 16:16:37 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.9865108E-05 3.1385422E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 16:16:38 3.434u 0.177s 0:03.87 93.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 16:16:38 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.864623 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -21.95800 35.12600 ymin,ymax (A): 55.13300 107.5630 zmin,zma (A): -2.364000 54.91300 x,y,z range (A): 57.08400 52.43000 57.27700 scale (grids/A): 1.864623 object centre (A): 6.584000 81.34800 26.27450 number of atom coordinates read : 3070 total number of charged atoms : 2928 net assigned charge : -3.499987 assigned positive charge : 457.8630 centred at (gu) : 92.80161 90.44024 89.95223 assigned negative charge : -461.3643 centred at (gu) : 92.84148 90.06886 90.33263 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27695 grid for indexing accessible points = 1.400000 m= 30010 mr = 57657 m= 4916 mr = 21407 m= 265 mr = 3064 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1031 time to turn everything in is 0.4200000 number of dielectric boundary points 37666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 22979 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6215410 object centre at (A) : 6.584000 81.34800 26.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9884152E-02 -2.1606330E-02 midg,1,midg; midg,igrid,midg -1.7299853E-02 -1.1814473E-02 1,midg,midg; igrid,midg,midg -1.5300289E-02 -4.7291532E-02 gauss-seidel spectral radius is 0.9986306 estimated iterations to convergence 214 setup time was (sec) 0.6400000 now iterating at: 16:16:38 rms-change max change #iterations 4.504934 172.8718 at 10iterations 2.094254 71.80580 at 20iterations 0.9781134 31.77019 at 30iterations 0.4573913 14.64266 at 40iterations 0.2131677 6.280367 at 50iterations 9.9521123E-02 2.814430 at 60iterations 4.6539858E-02 1.374435 at 70iterations 2.1797877E-02 0.7041817 at 80iterations 1.0218673E-02 0.3045759 at 90iterations 4.7729462E-03 0.1541419 at 100iterations 2.2347639E-03 6.7985535E-02 at 110iterations 1.0507437E-03 2.9835701E-02 at 120iterations finished qdiffx linear iterations at : 16:16:46 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.0507437E-03 2.9835701E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 16:16:46 7.940u 0.197s 0:08.47 95.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 16:16:46 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.796934 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -21.95800 35.12600 ymin,ymax (A): 55.13300 107.5630 zmin,zma (A): -2.364000 54.91300 x,y,z range (A): 57.08400 52.43000 57.27700 scale (grids/A): 2.796934 object centre (A): 6.584000 81.34800 26.27450 number of atom coordinates read : 3070 total number of charged atoms : 2928 net assigned charge : -3.499987 assigned positive charge : 457.8630 centred at (gu) : 94.20223 90.66015 89.92822 assigned negative charge : -461.3643 centred at (gu) : 94.26208 90.10332 90.49889 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 196229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27695 grid for indexing accessible points = 1.400000 m= 96425 mr = 140405 m= 35090 mr = 77132 m= 8730 mr = 27717 m= 1238 mr = 6561 m= 52 mr = 856 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 3580 time to turn everything in is 1.080000 number of dielectric boundary points 85076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 23422 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.864623 object centre at (A) : 6.584000 81.34800 26.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8018785 -0.2600952 midg,1,midg; midg,igrid,midg -0.2207301 -0.3039988 1,midg,midg; igrid,midg,midg -0.2127594 -0.6301048 gauss-seidel spectral radius is 0.9992758 estimated iterations to convergence 293 setup time was (sec) 1.330000 now iterating at: 16:16:48 rms-change max change #iterations 10.82248 313.8796 at 10iterations 6.477009 149.7132 at 20iterations 3.834416 87.58056 at 30iterations 2.259949 45.04874 at 40iterations 1.325083 26.17337 at 50iterations 0.7769620 15.54694 at 60iterations 0.4546054 8.621215 at 70iterations 0.2648020 4.866324 at 80iterations 0.1543712 3.261902 at 90iterations 8.9806668E-02 1.663774 at 100iterations 5.2261353E-02 1.025433 at 110iterations 3.0313723E-02 0.5547962 at 120iterations 1.7615950E-02 0.3282776 at 130iterations 1.0215033E-02 0.1692009 at 140iterations 5.9319558E-03 0.1101170 at 150iterations 3.4308650E-03 6.5470695E-02 at 160iterations 1.9927495E-03 3.5984039E-02 at 170iterations 1.1561021E-03 2.1942139E-02 at 180iterations finished qdiffx linear iterations at : 16:16:59 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.1561021E-03 2.1942139E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 16:17:00 13.016u 0.218s 0:13.59 97.2% 0+0k 0+0io 0pf+0w